Re: [PyMOL] select clipped atoms

Hi Johannes, My guess is that you missed that get_view[0:8] is a _column-major_ rotation matrix. Transpose it before using it. I decided to take a look at this problem for preparation of better clipping planes in PyMOL. I got it to work in PyMOL using Python, after much fussing about. Here's w

Re: [PyMOL] select clipped atoms

Hi Johannes, Coincidentally, I found myself in need of the same functionality the other day. I came up with this: from pymol import cmd def clipped_by(at,v): x,y,z = at.coord nz = v[2]*(x-v[12])+v[5]*(y-v[13])+v[8]*(z-v[14])-v[11] return nz > v[15] and nz < v[16] def clipped(

Re: [PyMOL] How to color aligned structures by equivalent SSE?

Hi all, > That's cool enough to be it's own script.  I'll add that to the > PyMOLWiki if I find the time. This is now a script on the PyMOLWiki (http://www.pymolwiki.org/index.php/HighlightAlignedSS). Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.ve

Re: [PyMOL] Selecting ASP and GLU

yeah, its true. We should work out a tutorial for this kind of things. Something where there is only one line of instruction and one line of command, like: 1) Download a file fetch pdb1.pdb 2) Select all ASP or GLU residues: select acids, resn ASP+GLU 3) Suggestions? Am 02.03.11 22:36, s

Re: [PyMOL] How to color aligned structures by equivalent SSE?

Hi Eric, On Wed, Mar 2, 2011 at 1:41 PM, Eric Schreiter wrote: > I'm looking for a quick way to color two superimposed structures such that > SSEs for which there is an equivalent in both structures are colored and the > non-matching SSEs and loops are grey.  Also, the colored SSEs would be >

Re: [PyMOL] Selecting ASP and GLU

On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote: > Hey :) > > It's good to note that programs are written by programmers, using > programmer's logic. First of all, I was not complaining about the logic of the PyMOL programmers. I tried to help find out the reason that might cause Martin's script

Re: [PyMOL] Rendering Large Scene Crashes Pymol

Hi Ian & Tsjerk, > You can try to set hash_max (set hash_max,200) to put a limit on memory > usage. Then again, an immediate crash can also mean the scene just isn't > going to fit in memory. Complex scenes I usually write in parts to povray > format, which I then combine and raytrace with povray.

Re: [PyMOL] select clipped atoms

Hi, I implemented the coordinate transformation and the selection of atoms outside PyMol, in R. In principle it works, but there seems to be some error, since too many atoms are selected, corresponding roughly, but not completely to an enlarged clipping corridor between the planes defined by

Re: [PyMOL] Selecting ASP and GLU

Hey Hongbo, good way of putting it. Indeed, I think thats what seemed most intuetively to me in the beginning, and so I ended up trying to figure out why 'AND' was not giving me the expected selection. Remembering my boolean algebra lecture from back in the days, I suddendly realized that it ha

Re: [PyMOL] Selecting ASP and GLU

Hey :) It's good to note that programs are written by programmers, using programmer's logic.The confusion is not so much caused by the simplified expression, but by users with little background in mathematics/logic assessing 'and' and 'or' from a linguistic background. In computer science and math

[PyMOL] FW: help

Hi, I have couple of questions for you, which could be very silly. I downloaded the movie.py from http://www.rubor.de/, which is rTools 0.7.2 and put it to the right directory. When I did run movie.py, nothing seemed wrong. And then I did mv_clear, and still good. But when I do like : mv_move 1

Re: [PyMOL] R: Re: Re: labeling by a pseudoatom

Hi Martin, You're in the wrong thread! In addition, + is not OR. OR merges expressions, + 'merges' identifiers in an expression. Further, in the code you gave it said 'or'. It seems from this post you wrote 'and' in your script, signifying a mismatch between what you were doing and what you though

[PyMOL] How to color aligned structures by equivalent SSE?

I'm looking for a quick way to color two superimposed structures such that SSEs for which there is an equivalent in both structures are colored and the non-matching SSEs and loops are grey. Also, the colored SSEs would be rainbow (e.g. the first matching SSE colored blue, second colored green,

Re: [PyMOL] Selecting ASP and GLU

I believe the confusion is caused by the simplified selection expression in PyMOL (and some other visualization tools as well). I remember that one of my colleagues once questioned strongly the reason of using OR instead of AND in such situation. The expression: select resn GLU or resn ASP ac

[PyMOL] Question about the .obj file saved by Pymol

Hello, If I use "save myscene.obj" and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F.

Re: [PyMOL] Rendering Large Scene Crashes Pymol

Hi Ian, You can try to set hash_max (set hash_max,200) to put a limit on memory usage. Then again, an immediate crash can also mean the scene just isn't going to fit in memory. Complex scenes I usually write in parts to povray format, which I then combine and raytrace with povray. Hope it helps,

Re: [PyMOL] R: Re: Re: labeling by a pseudoatom

Dear all thanks for the feedback. Indeed, after thinking for a second its totally clear why 'select identifyer, (resn asp and resn glu)' returns { }. So, speaking of syntax, '+' is OR and '&' is AND? Thanks again Martin Am 02.03.11 01:35, schrieb rv...@libero.it: > Hi Jason, > sorry for la

[PyMOL] Rendering Large Scene Crashes Pymol

I am trying to Render out a very large scene in pymol, on a 64-bit windows 7 computer, and as soon as I try and raytrace, pymol crashes with no useful error message. I tried creating a pov file, and rendering with pov-ray, but pymol still crashed. What are my options for rendering out my scene, if

[PyMOL] Question about the .obj file saved by Pymol

Hello, If I use "save myscene.obj" and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F.

[PyMOL] R: Re: Re: labeling by a pseudoatom

Hi Jason, sorry for last message .. To label a residue by an mdo command cmd.mdo(int frame, string command) I can pass as command one among these strings: 1) 'label %s, "%s %s"' % (..) works fine but prints a message (I don't want) to the output window 1+) 'label %s, "%s %s", quiet=1' %

Re: [PyMOL] Selecting ASP and GLU

Hi, Seems to work fine for me. I'm using version 1.3, although I doubt that this could be a version compatibility problem. Could you give more specifics on how it doesn't work for you (ASPs not colored red or GLUs not colored red, etc.) ? Note that the parenthesis around 'resn glu' aren't needed.

Re: [PyMOL] Selecting ASP and GLU

For me, color red, resn asp+glu works. Maia Martin Hediger wrote: > Dear all > What is the selection syntax to select all GLU and ASP residues within > an object? > > I'm trying it the way its written on the wiki: > remove resn hoh# remove water > h_add # add hydrogens > > a